konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network
Proteins work in coordination to catalyze and regulate all biological activities and drive cellular functions. The collective behavior of proteins is studied through protein-protein interaction (PPI) networks, which provide a system-level understanding of their regulatory behavior. konnect2prot (k2p...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037025002697 |
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| author | Shivam Kumar Abhinav Agarwal Dipanka Tanu Sarmah Samrat Chatterjee |
| author_facet | Shivam Kumar Abhinav Agarwal Dipanka Tanu Sarmah Samrat Chatterjee |
| author_sort | Shivam Kumar |
| collection | DOAJ |
| description | Proteins work in coordination to catalyze and regulate all biological activities and drive cellular functions. The collective behavior of proteins is studied through protein-protein interaction (PPI) networks, which provide a system-level understanding of their regulatory behavior. konnect2prot (k2p) is a web application that generates a context-specific directional PPI network from a list of proteins as input. It identifies influential spreaders in the generated network and detects their biological and topological importance. Here, we report the features added to k2p since its first release. Building on the foundation of its predecessor, k2p 2.0 now integrates differential gene expression analysis, thereby bridging the gap between gene-level regulation and protein-level activity, providing a holistic view of how transcriptional changes fuel cellular behavior. konnect2prot 2.0 is freely accessible at: https://konnect2prot_v2.thsti.in. |
| format | Article |
| id | doaj-art-b0c7622bb1fb4bc4adc13cbe305b672c |
| institution | DOAJ |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-b0c7622bb1fb4bc4adc13cbe305b672c2025-08-20T03:17:46ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-01273036304410.1016/j.csbj.2025.07.006konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction networkShivam Kumar0Abhinav Agarwal1Dipanka Tanu Sarmah2Samrat Chatterjee3Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, IndiaComplex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, IndiaSystems Biology Ireland, University College Dublin, Dublin, IrelandComplex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India; Corresponding author.Proteins work in coordination to catalyze and regulate all biological activities and drive cellular functions. The collective behavior of proteins is studied through protein-protein interaction (PPI) networks, which provide a system-level understanding of their regulatory behavior. konnect2prot (k2p) is a web application that generates a context-specific directional PPI network from a list of proteins as input. It identifies influential spreaders in the generated network and detects their biological and topological importance. Here, we report the features added to k2p since its first release. Building on the foundation of its predecessor, k2p 2.0 now integrates differential gene expression analysis, thereby bridging the gap between gene-level regulation and protein-level activity, providing a holistic view of how transcriptional changes fuel cellular behavior. konnect2prot 2.0 is freely accessible at: https://konnect2prot_v2.thsti.in.http://www.sciencedirect.com/science/article/pii/S2001037025002697Konnect2prot 2.0Expression analysisDEG analysisNetwork AnalysisVisualizationEnrichment |
| spellingShingle | Shivam Kumar Abhinav Agarwal Dipanka Tanu Sarmah Samrat Chatterjee konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network Computational and Structural Biotechnology Journal Konnect2prot 2.0 Expression analysis DEG analysis Network Analysis Visualization Enrichment |
| title | konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network |
| title_full | konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network |
| title_fullStr | konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network |
| title_full_unstemmed | konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network |
| title_short | konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network |
| title_sort | konnect2prot 2 0 integrating advanced analytical tools for deeper understanding of protein properties in a functional protein protein interaction network |
| topic | Konnect2prot 2.0 Expression analysis DEG analysis Network Analysis Visualization Enrichment |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025002697 |
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